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Zinc in PDB 2ckr: X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose

Enzymatic activity of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose

All present enzymatic activity of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose:
3.2.1.4;

Protein crystallography data

The structure of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose, PDB code: 2ckr was solved by G.I.Berglund, P.J.Gualfetti, C.Requadt, L.S.Gross, T.Bergfors, A.Shaw, M.Saldajeno, C.Mitchinson, M.Sandgren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.11 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.365, 70.850, 76.278, 90.00, 93.86, 90.00
R / Rfree (%) 15.8 / 19.3

Other elements in 2ckr:

The structure of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose (pdb code 2ckr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose, PDB code: 2ckr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 2ckr

Go back to Zinc Binding Sites List in 2ckr
Zinc binding site 1 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1433

b:12.3
occ:1.00
 OD1 A:ASP169 1.9 14.6 0.7
OD1 A:ASP173 1.9 12.6 1.0
OD1 A:ASP169 2.0 11.8 0.3
CG A:ASP173 2.8 9.9 1.0
CG A:ASP169 2.9 13.1 0.7
OD2 A:ASP173 2.9 9.8 1.0
OD2 A:ASP169 3.0 16.1 0.7
CG A:ASP169 3.2 11.8 0.3
OD2 A:ASP169 3.5 12.4 0.3
NH2 A:ARG216 3.8 17.5 1.0
O A:HOH2035 4.0 26.9 1.0
O A:ASP169 4.2 11.0 0.3
CB A:ASP173 4.2 8.7 1.0
CB A:ASP169 4.2 12.1 0.7
O A:ASP169 4.3 10.6 0.7
CB A:ASP169 4.4 11.5 0.3
C A:ASP169 4.6 11.1 0.3
C A:ASP169 4.6 11.2 0.7
CZ A:ARG216 4.6 16.4 1.0
NE A:ARG216 4.8 15.8 1.0
CA A:ASP169 4.8 11.8 0.7
CA A:ASP169 4.8 11.5 0.3

Zinc binding site 2 out of 5 in 2ckr

Go back to Zinc Binding Sites List in 2ckr
Zinc binding site 2 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1434

b:26.8
occ:0.50
 OD1 A:ASP289 2.2 15.2 0.6
O A:HOH2271 2.2 22.7 1.0
OD1 A:ASP287 2.2 18.1 1.0
O A:ALA251 2.4 15.3 1.0
CG A:ASP289 3.2 14.7 0.6
CG A:ASP287 3.4 15.8 1.0
OD2 A:ASP289 3.4 18.4 0.6
C A:ALA251 3.5 14.6 1.0
O A:LYS253 3.6 12.6 1.0
O A:HOH2159 3.6 25.8 1.0
OD2 A:ASP287 3.8 18.9 1.0
O A:HOH2162 3.8 25.9 1.0
OG A:SER290 4.0 13.2 0.3
CA A:ALA251 4.2 14.2 1.0
CB A:ASP289 4.5 12.9 0.6
CB A:ASP287 4.6 13.2 1.0
N A:SER252 4.6 15.0 1.0
N A:ASP289 4.6 12.5 0.6
O A:HOH2129 4.7 19.1 1.0
CA A:ASP287 4.7 12.8 1.0
C A:LYS253 4.7 12.8 1.0
N A:SER290 4.8 12.7 0.3
N A:SER290 4.8 12.9 0.7
CB A:ALA251 4.9 14.3 1.0
CA A:SER252 4.9 15.5 1.0
C A:ASP287 4.9 12.4 1.0
C A:SER252 4.9 14.8 1.0
CA A:ASP289 4.9 13.1 0.6

Zinc binding site 3 out of 5 in 2ckr

Go back to Zinc Binding Sites List in 2ckr
Zinc binding site 3 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1437

b:11.7
occ:1.00
 OD1 B:ASP173 1.9 12.6 1.0
OD2 B:ASP169 1.9 11.6 0.7
OD1 B:ASP169 2.1 10.1 0.3
CG B:ASP173 2.8 10.1 1.0
CG B:ASP169 2.9 12.3 0.7
OD2 B:ASP173 2.9 9.8 1.0
CG B:ASP169 3.1 11.2 0.3
OD1 B:ASP169 3.1 14.1 0.7
OD2 B:ASP169 3.2 11.0 0.3
NH2 B:ARG216 3.8 18.1 1.0
O B:HOH2030 3.9 24.7 1.0
O B:ASP169 4.1 10.9 0.3
CB B:ASP173 4.2 8.4 1.0
O B:ASP169 4.2 10.7 0.7
CB B:ASP169 4.3 11.6 0.7
CB B:ASP169 4.5 11.2 0.3
C B:ASP169 4.6 11.0 0.3
CZ B:ARG216 4.6 17.2 1.0
C B:ASP169 4.6 10.9 0.7
NE B:ARG216 4.8 16.7 1.0
CA B:ASP169 4.8 11.6 0.7
CA B:ASP169 4.8 11.3 0.3

Zinc binding site 4 out of 5 in 2ckr

Go back to Zinc Binding Sites List in 2ckr
Zinc binding site 4 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1438

b:23.5
occ:1.00
 NE2 B:HIS146 1.9 17.6 1.0
OE2 B:GLU145 2.1 20.6 1.0
CE1 B:HIS146 2.8 18.8 1.0
CD2 B:HIS146 3.0 18.2 1.0
CD B:GLU145 3.1 18.3 1.0
CG B:GLU145 3.4 17.3 1.0
ND1 B:HIS146 3.9 18.3 1.0
CG B:HIS146 4.1 17.7 1.0
OE1 B:GLU145 4.2 20.1 1.0
O B:HOH2013 4.9 24.5 1.0
CB B:GLU145 4.9 16.8 1.0

Zinc binding site 5 out of 5 in 2ckr

Go back to Zinc Binding Sites List in 2ckr
Zinc binding site 5 out of 5 in the X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of X-Ray Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A (E5) E355Q in Complex with Cellotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1439

b:29.4
occ:0.50
 OD1 B:ASP289 2.1 18.9 0.7
O B:HOH2263 2.2 36.8 1.0
OD1 B:ASP287 2.2 18.7 1.0
O B:ALA251 2.5 15.1 1.0
O B:HOH2157 3.1 27.8 1.0
CG B:ASP289 3.1 17.7 0.7
CG B:ASP287 3.3 16.4 1.0
OD2 B:ASP289 3.4 21.6 0.7
O B:LYS253 3.4 13.9 1.0
O B:HOH2154 3.5 27.1 1.0
OD2 B:ASP287 3.6 18.2 1.0
C B:ALA251 3.6 14.7 1.0
CA B:ALA251 4.2 14.2 1.0
O B:HOH2127 4.4 13.3 1.0
CB B:ASP289 4.5 16.1 1.0
CB B:ASP287 4.5 13.3 1.0
C B:LYS253 4.6 13.4 1.0
N B:ASP289 4.6 14.7 1.0
N B:SER252 4.7 14.7 0.4
N B:SER252 4.7 14.8 0.6
CA B:ASP287 4.7 13.1 1.0
N B:SER290 4.8 14.8 1.0
C B:ASP289 4.8 15.6 1.0
CA B:ASP289 4.8 15.8 1.0
O B:HIS250 4.9 12.2 1.0
C B:SER252 4.9 14.8 0.6
C B:ASP287 4.9 12.8 1.0
CB B:ALA251 4.9 14.5 1.0
CE B:LYS134 5.0 21.6 1.0
C B:SER252 5.0 14.5 0.4

Reference:

G.I.Berglund, P.J.Gualfetti, C.Requadt, L.S.Gross, T.Bergfors, A.Shaw, M.Saldajeno, C.Mitchinson, M.Sandgren. The Crystal Structure of the Catalytic Domain of Thermobifida Fusca Endoglucanase CEL5A in Complex with Cellotetraose To Be Published.
Page generated: Wed Oct 16 22:24:58 2024

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